cSSMD: Assessing collective activity for addressing off-target effects in genome-scale RNA interference screens

doi:10.1093/bioinformatics/btr474

UM > Faculty of Health Sciences

	cSSMD: Assessing collective activity for addressing off-target effects in genome-scale RNA interference screens
	Zhang X.D.1 ; Santini F.1; Lacson R.1; Marine S.D.1; Wu Q.2; Benetti L.4; Yang R.1; McCampbell A.1; Berger J.P.1; Toolan D.M.1; Stec E.M.1; Holder D.J.1; Soper K.A.1; Heyse J.F.1; Ferrer M.3
	2011-10-01
Source Publication	Bioinformatics
ISSN	13674803 14602059
Volume	27 Issue:20 Pages:2775-2781
Abstract	Motivation: Off-target activity commonly exists in RNA interference (RNAi) screens and often generates false positives. Existing analytic methods for addressing the off-target effects are demonstrably inadequate in RNAi confirmatory screens. Results: Here, we present an analytic method assessing the collective activity of multiple short interfering RNAs (siRNAs) targeting a gene. Using this method, we can not only reduce the impact of off-target activities, but also evaluate the specific effect of an siRNA, thus providing information about potential off-target effects. Using in-house RNAi screens, we demonstrate that our method obtains more reasonable and sensible results than current methods such as the redundant siRNA activity (RSA) method, the RNAi gene enrichment ranking (RIGER) method, the frequency approach and the t-test. © The Author 2011. Published by Oxford University Press. All rights reserved.
DOI	10.1093/bioinformatics/btr474
URL	View the original
Language	英語
Fulltext Access	View Full-Text via DOI View Full-Text via Web of Science View Full-Text via Scopus
Citation statistics	Cited Times [WOS]:14 [WOS Record] [Related Records in WOS]
Document Type	Journal article
Collection	Faculty of Health Sciences
Affiliation	1.Merck Research Laboratories 2.University of Pennsylvania 3.National Institutes of Health, Bethesda 4.Merck & Co., Inc.
Recommended Citation GB/T 7714	Zhang X.D.,Santini F.,Lacson R.,et al. cSSMD: Assessing collective activity for addressing off-target effects in genome-scale RNA interference screens[J]. Bioinformatics,2011,27(20):2775-2781.
APA	Zhang X.D..,Santini F..,Lacson R..,Marine S.D..,Wu Q..,...&Ferrer M..(2011).cSSMD: Assessing collective activity for addressing off-target effects in genome-scale RNA interference screens.Bioinformatics,27(20),2775-2781.
MLA	Zhang X.D.,et al."cSSMD: Assessing collective activity for addressing off-target effects in genome-scale RNA interference screens".Bioinformatics 27.20(2011):2775-2781.

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